Rei and Shinji's Sister Act
by Author0fntent
Summary: In the aftermath of the final battle of Tokyo-3, three intact Rei clones are discovered in a hidden room of Terminal Dogma. What will become of them? Inspired partly by Neon Genesis Evangelion -ANIMA-.
1. Chapter 1

**Tokyo-3, late 2015...**

The nightmare was over, at long last. And whatever greater nightmare, whether envisioned by the men of the SEELE council, or Gendo Ikari, would never come to pass. NERV had won their deadliest fight, not against an Angel, but a human enemy. But the victory was not without cost. A number of civilian casualties had to be accounted for, but thankfully there were a good number of survivors. More than that, something would be done about the psychological toll it'd taken on everyone involved, especially the teenage pilots of the Evangelions.

One of them, at the moment, was helping with clearing the wreckage of the Geofront. Shinji had used the massive hands of Unit-01 to save a spot of greenery that had somehow remained unscathed: Kaji's watermelon patch. With a thought, the giant moved the patch to a truck bed that was nearby. Maybe then they could properly move it to a better place.

_And give him something to come back to aside from Misato_, he thought to himself. Shinji was experiencing a number of feelings at the moment, mostly relief, but for now, he was just tired. Tired of the fighting, the pain, the horrors. He could rest easy now, since it was finally finished. Maybe then he could start to actually live his life. Among his top three of things he'd immediately do, was to apologize and make amends with Asuka, and then Rei. After that, talk with Misato, to try and move past the moment before she shoved him into the EVA cage. Speaking of, Misato's voice crackled to life on the entry plug's comms.

"Shinji? Got a minute?" she asked.

Shinji smiled. He'd been worried, considering the last time he saw her, she'd been protecting him from a bloodthirsty JSSDF squad. He was afraid she didn't make it.

"What's up, Misato?" he responded.

"We need you back here and out of Unit-One. Ritsuko...found something. Something that you need to see," she said.

"...Yes, Misato. Right away," he replied as he started moving in the direction of the partially-ruined edifice of NERV HQ.

It was quite a turn of events, really; the one thing in his scenario that his father hadn't counted on was Rei developing a conscience, one that spurred her to react quickly and shove Ritsuko out of the way of Gendo's shot, the moment he tried to execute her. In turn, it allowed Ritsuko to fire off her own shot, which got him in the leg; she fired off an additional one that rendered his arm useless. Taking Rei and fleeing from Terminal Dogma, she'd then activated the reprogrammed explosives to go off only in the Chamber of Gauf. Some time after the battle above had finished, a recovery team had found Gendo under all the rubble, somehow still clinging to life. While apprehended, Ritsuko personally removed the embryonic form of Adam from his palm and, with a shard recovered from one of the lances used by the EVA series, killed it with one stroke.

Shinji eventually found a good place to 'park' Unit-01, and lowered it so he had an angle to climb out. Once done, he walked over to the front entrance to the main building of HQ. Misato, patched up thanks to the medical team only a few hours before, was waiting for him, as was Asuka, looking hauntingly exhausted. No wonder, considering the ordeal she'd gone through, culminating in a very brutal battle with the EVA series. A tense air was present between them; they'd already indicated that when they had a moment's peace, they were going to have a long, long talk. The three then proceeded on their way to Terminal Dogma, past the weary-looking Makoto and Shigeru, who were tending to the shell-shocked Maya. Soon they were in the elevator heading downward, until they reached their destination. Once the doors opened, they continued on till they reached the room Ritsuko had directed them to, where she and Rei were waiting for them.

Surprisingly, it was Asuka who said the first thing out of all of them.

"...You okay, Wondergirl?" she asked.

Rei, for once, showed a bit of mild surprise at Asuka, considering the last time they'd spoken to one another. "I...I am unharmed. Are you all right?"

What Asuka answered with took everyone else further aback. "...Not really. But I'll manage for now."

Ritsuko chose that moment to clear her throat, getting the attention of all three pilots.

"Before I show you this, I want to...On behalf of all of us, I really want to apologize," she said. "For everything we put you through." She looked at Rei specifically. "For how we've treated you all this time. Nothing can truly make up for what we deprived you of when we essentially drafted you to fight our battles. But I truly hope that we can help you regain some sense of a normal life." She then knelt down in front of Rei. "Or in your case, actually give you a normal life. Rei, I...I'm so, so sorry for how I treated you in particular. I wouldn't hold it against you if you couldn't forgive me."

Further adding to the day's minor surprises, Rei put her hand on Ritsuko's shoulder. "It is not your fault," she said. "I remember...something your mother said. There is some truth to it-to the Commander, we were both tools. But now, we no longer need to feel as such." Uncharacteristically of her, Rei then hugged an astonished Ritsuko; after a brief moment of hesitation, Ritsuko returned the hug.

"What was it you wanted us to see, doctor?" Shinji asked.

Ritsuko stood back up before responding. "It has to do with...what I showed you and Misato, after the Sixteenth Angel was defeated."

"What're you talking about?" Asuka asked, confused. Ritsuko motioned them to follow her further into the room as she, Shinji and Misato explained to Asuka Rei's origins, and how Ritsuko, in the midst of a breakdown in front of the two, destroyed the tank full of Rei clones. Asuka was speechless upon hearing this, and at the same time, felt great pity and remorse over how she herself treated Rei. Soon they reached the object of their curiosity, which took all but Ritsuko by surprise.

In front of them were three pods, filled with LCL. Within them were three Rei clones.

"But how?" Shinji wondered. "Misato and I-we saw you-"

"I thought the same thing," Ritsuko said. "But then I found this room while Rei and I fled from the epicenter of the collapse in the Chamber of Gauf. If I had to hazard a guess, I'd say the Commander was paranoid enough to think I'd pull something like dissolving the clones. He must have secreted these three away, just in case."

The four took another look at the trio of clones. They noticed some slight differences between them compared to Rei herself. The middle clone, labeled 'Rei-Quatre', was the one who definitely looked the most similar to Rei, save for her silvery hair color. The one on the left, labeled 'Rei-Cinq', was a bit taller, looking as if she'd be at least a couple of years older than Shinji and Rei. The one on the right, 'Rei-Six', was the youngest, looking like an elementary school kid. To Rei, it looked like the very first incarnation of herself, at the same age when she met her untimely demise at Naoko Akagi's hands.

"...What're you planning to do with them?" Misato asked.

Ritsuko looked at her friend solemnly as she answered. "At the moment, I don't know. Like I said before, they're just empty vessels. They couldn't survive out in the world the way they are."

A look of realization then emerged on Rei's face. "I...might have an idea," she said.

"You do?" Shinji asked.

"Yes," she replied. "I will need to see Lilith."

**END Part 1.**

****Author's Note(s)**  
I got my idea for this after reading the English translation of the first volume of ****_-ANIMA- _****this month, and given what happens to the cast in that story, I started thinking of a more...brighter outcome for them, which I'll elaborate more on in the two chapters that follow.**


	2. Chapter 2

**Tokyo-3, March 2017...**

A warm aroma filled the kitchen as Shinji prepared breakfast. He wasn't alone in his endeavor, as Rei set the table while another occupant of the apartment helped him cook.

"How're the eggs coming along?" Shinji asked while he finished slicing up some fruit.

"Almost finished," replied Shinko Ikari. "Rei, when you're done setting the table, could you try and pry Kira and Seika out of bed?"

"Yes, sister," Rei answered as she set the last plate down. She then walked through the hallway until she reached a certain door, and knocked on it to stir the two occupants awake.

"Kira! Seika! Breakfast is almost ready, will you please get up?" she called from outside the door. From behind it, she could hear some small grumbles.

"Jus' five more minutes..." groaned Seika Ikari.

"But soft, methinks I scent the morning air..." mumbled Kira Ikari.

Rolling her eyes, Rei decided it was time for desperate measures. Slowly opening the door to her two sisters' room, she then let out a loud whistle that immediately jolted them awake, with Kira landing all tangled up in her covers on the floor.

"*UGH* Have I thought long to see this morning's face, and doth it give me such a sight as this?" Kira muttered as she worked to untangle herself.

"Awww, I was having a good dream!" bemoaned Seika as she rubbed her eyes.

"I am sure you will have it again later tonight," Rei said. "But right now, it would be prudent for you-both of you-to join us at the table. So please wash up before you come in."

At that, Seika was quickly out the door and in the bathroom. "INBEFOREKIRA!" she quipped before she closed the door. Kira merely looked at Rei, bleary-eyed as she stretched and yawned. "One day I'll find out how she does that," she said as she went to wait outside the bathroom door.

Soon enough, both Seika and Kira joined the others at the table, a delicious-looking breakfast awaiting them. Thankfully for Shinji, unlike Rei, the other three had more omnivorous diets, though he still made a pretty good vegetarian omelette for Rei. Shinji took a moment to look around at his surroundings and the people in them, still feeling amazed at how it got to this point.

On that day two years ago, he and Rei had entered the Chamber of Gauf and appealed to Lilith. The threat of a Third Impact was gone, and she no longer need fear the misuse of her power at the hands of others. Touched by their concern and what they had endured, the Second Angel returned to her real form and gave them the boon they asked of; that is, provide the three Rei clones with souls of their own, allowing them each to be their own person. Lilith went a couple of extra miles and even removed their S2 organs, along with Rei's, making all four fully human. Before she left the chamber for parts unknown, she also did the planet a small favor and returned it to its original axis. With that, Lilith vanished. Shinji and Rei then returned to the room they'd been in, where Ritsuko and the others had emptied the pods and helped the newly-awakened clones get their bearings. It was decided, among them, that the three clones would live with Shinji and Rei, considering they were the only other (free) living relatives they could rely on. A little help from Kaji, who'd come out of hiding after working to expose both SEELE's and Gendo Ikari's plans to the world, got the girls some official backgrounds and papers, with medical records provided by Ritsuko. In the two years since, the quintet had become a close family. And it was quite a family Shinji and Rei had found themselves with.

Shinko, the clone previously dubbed Rei-Cinq, proved to be as much the responsible big sister, though she never lorded her 'authority' over her other siblings, working in tandem with Shinji and Rei to keep their house in order. She also had the longest hair of the four girls, and had dyed it a light purple, 'for contrast' in her own words. She was two years ahead of Shinji and Rei at the high school they attended, and proved to be a favorite among the teachers, though not to the point of her being labeled a 'teacher's pet'.

Kira, Rei's silver-haired, mostly-identical twin (and formerly Rei-Quatre), was every bit the Bohemian theater geek, laid back and able to call up the lines of many a famous playwright on-demand, with Shakespeare her most-utilized; her personal bookshelf alone boasted a good number of scripts and screenplays, well-worn from many a re-read. Which came in very handy for her as a member of the school drama club, which was going to be putting on a production of _Much Ado About Nothing_ in a few weeks. And she didn't limit her repertoire to just playwrights, since her wit was also formed on a small diet of beat poetry books she'd gotten from a used bookstore a while back.

Seika, the littlest Ikari (known before as Rei-Six), was a bona-fide hyperactive, tomboyish grade-schooler who became great friends with Sakura Suzuhara and Nozomi Horaki. Just as Asuka dubbed Shinji, Toji and Kensuke the Three Stooges, Hikari dubbed the three little girls the 'tiny triumvirate of terror', since together those three made themselves the banes of their respective siblings' existence. (And they knew how to effectively weaponize their cuteness.) Seika kept most of her short hair its natural blue, with the exception of an auburn streak on the left side of her bangs.

Shinji and Rei underwent a few changes of their own in those same two intervening years. Shinji let his hair grow out a little more, to the point where he now wore a ponytail; a little ribbing from Kaji had ensued, which included, among other things, him dubbing Shinji 'Mini-Me'. (Having never seen those particular movies, the joke was a bit lost on Shinji.) Shinji took very well to being a big brother to Seika, being the more fun-loving one between himself and Rei. Rei also grew her hair out a bit, though not as long as Shinko's. She'd learned to be a bit more expressive with her emotions, though she still hadn't yet conquered the realm of contractions. Being a sibling, older or middle or otherwise, proved to be an interesting experience for the former introvert, one that she was greatly enjoying.

"Delicious, as always, dear brother," Kira fancifully declared, "though one doth wonder how much of yon efforts comprises thee compared to fair Shinko."

"Are you saying Shinko's a better cook than me?" Shinji teasingly asked.

"Mere inference, 'tis all," Kira replied as she put another forkful of eggs in her mouth.

"How long is Kira going to keep talkin' like that?" Seika asked.

"Until they finally get the play over with," Rei replied.

"Or at least until she visits Stratford-Upon-Avon," Shinko added.

This elicited a bit of a chuckle among everyone but Seika, who didn't get it. Once everyone ate, Seika and Kira went back to shower and get dressed while the others made lunches for school. While they were halfway done, the doorbell rang, which Shinko answered. Sure enough, on the other side of the door was someone they'd come to regularly expect.

"_Morgen_, Shinko," Asuka greeted.

**END Part 2.**


	3. Chapter 3

"Good to see you, Asuka," Shinko said as the two exchanged a quick hug. She then stepped inside and did the same with Rei, before planting a good morning kiss on Shinji.

Asuka underwent quite the transformation herself in those two years, probably more so than her fellow pilots. Taking into account the things she'd gone through in the later stages of the Angel War, and what her own childhood had consisted of, if anyone was in the most dire need of professional help, it was Asuka. No longer letting her pride get in the way, she was the first to sign up for the counseling offered in the aftermath of the battle. She, Shinji and Rei wound up in a series of group sessions together, which enabled them to finally air their grievances, figure out where they stood from there, and help each other hopefully move forward. (An additional anger management session also greatly helped her; she also found an outlet to channel her aggression after joining the school's Kendo team.) For her and Shinji especially, reconciling their respective feelings for one another took some doing, but going slowly helped them open up more and more. The two were together ever since, much to the 'chagrin' of Shinji's two fellow stooges once they returned to the city. Asuka also made a bit of a stylistic choice in that she stopped wearing her A-10 connectors, realizing that her life didn't need to be defined by her being an EVA ace. It took some doing, but Asuka was growing into a more patient, better-adjusted young woman.

At that moment, both Kira and Seika stepped back into the living room, now each clad in their respective school uniforms. Seika beamed a big smile when she saw the new arrival.

"Asuka!" she said as she practically jumped into a hug.

"Morning, squirt," Asuka replied as she lightly ruffled the girl's hair. Seika looked up to Asuka as something of another big sister, and the former EVA-02 pilot took it in stride. "Make any progress on _Golden Sun_?"

Seika nodded affirmatively. "Already on the Fuchin Temple!" she eagerly answered, making Asuka smirk. She'd given Seika the game for her birthday only a short while ago.

Soon enough, Shinji and Rei had everyone's lunches packed, and everyone piled out of the apartment, followed by Rei locking the door. Soon enough, the sextet were greeted by the sight of their next-door neighbors heading out for another day of drudgery. Said neighbors being, for the better part of a year now, the happily-married Mister and Missus Ryoji Kaji, both of whom Asuka's current foster parents.

"Hey guys," Misato said as she greeted Shinji and his sisters. The ever-present Pen-Pen poked his head out the door, causing Seika to give him a scratch above his beak, making him tap his foot repeatedly.

In the aftermath of the last battle, once the initial investigations had been conducted, it was decided by the UN that NERV would continue on in a limited capacity, focusing on not only the destruction of the Evangelions and any remaining Angelic material, but also in freeing Yui Ikari and Kyoko Zeppelin Sohryu from the cores of the now-decommissioned Units-01 and 02. (By a stroke of luck, Yui and Kyoko were guiding the efforts after those on the outside discovered a means for them to communicate from within the cores.) Kozo Fuyutsuki, worn out from all the conflict, had opted for retirement, leading Misato to be selected as the new commander of NERV, with Kaji acting as vice-director. The two had also negotiated something of a 'work-release' arrangement for Ritsuko, making the case that she was an unwilling party to Gendo Ikari's and SEELE's machinations. Their leadership was a much-needed change of pace from the command structure of two years prior. In that time, the two had tied the knot, and were appointed Asuka's long-term guardians, after she made it apparent that she was done with the father who'd essentially abandoned her. These days, Misato and Ryoji had another thing on their minds besides the bureaucratic navigation that their current positions entailed: Misato herself was currently three months pregnant with their first child.

"Morning," Shinji replied as the group started making their way to the elevator. "The grindstone beckons?"

"Oh yeah," his former guardian replied. "I'm starting to think I got off lightly when I was ops director. Compared to the paperwork I used to do, they've practically got me rock-climbing everyday."

"I'm also getting a good idea of what Fuyutsuki had to put up with for all those years," Kaji added, inferring his thoughts on his share of the paperwork he and Misato had to plow through most of the time.

The conversation kept going as they took the elevator down and made their way to the front of the apartment building, at which point the commanders made their way to Misato's car, which had finally gotten a much-needed repair job. Reluctantly, given her current state, she'd ceded all driving duties to Ryoji, much to his relief. (And the collective relief of nearly everyone in the city.)

"Say hi to the pair-o'-docs for us, will ya?" Asuka implored as she and the others waved goodbye.

"Will do!" the Kajis said as the car started.

Asuka was referring to, of course, Ritsuko and Maya, the latter of whom had pursued and gotten her doctorate in the intervening years. On the day the clones had been found, when they'd returned to the bridge, Maya abruptly got up where she'd been sitting, ran up to Ritsuko and kissed her passionately, confessing her feelings at last. Ritsuko, bewildered at first, surprised everyone when she returned it, Maya's kiss in effect causing her to have an epiphany right on the spot. The two took it slowly as they eased into their new relationship, and everyone proved to be happy for them. Rits sponsored Maya's doctoral pursuit, and once in-hand the two of them were put in charge of the efforts to free Yui and Kyoko.

The sextet of students continued on until they reached the building that was Seika's elementary school, where they were met by a quartet of familiar faces: Toji and Sakura Suzuhara, and Hikari and Nozomi Horaki. Toji and Hikari had gotten closer while they'd been away from the city, with Hikari mellowing out a bit more. When they'd returned, Toji set about volunteering at a rehab center for people with prosthetic limbs, which he genuinely felt good about. He'd cleared the air with Shinji long before then, giving both some sense of closure over the Unit-03 incident.

The three little girls immediately and eagerly convened, exchanged their (patent pending) secret handshake-something the older kids still couldn't crack-and quietly exchanged a few small goodies to slip into their siblings' bentos, guaranteed to result in something hilarious. They then started making their way through the front gates of the school, waving their siblings and Asuka off.

"See you after school!" they all said simultaneously, before a case of the giggles overtook them. Said giggles inspired a tiny pang of worry in Shinji, Toji and Hikari.

"Should we be afraid...?" Toji asked as he rubbed the back of his head.

"Knowing those three, _definitely_," Hikari answered.

"I'm sure it'll be priceless," Asuka said with a smirk.

"And that Kensuke will be sure to get it on film," Rei added, referring to their bespectacled otaku friend. In the intervening years, he'd decided to use his shutterbug skills for good as a photographer for the school paper.

"Oh heavens, trust them-surely they wouldn't!" Kira chimed in while waving a hand dismissively. "_There's no more faith in thee than in a stewed prune._"

Shinko merely chuckled, which proved to be contagious as the rest followed her lead as they continued towards the high school. As they walked along, Shinji took another look at the scene he was in, surrounded by friends and loved ones, hand-in-hand with Asuka. Life hadn't been peachy for him two years ago, so he now treasured every bit of his present. He had a girlfriend who loved him, dependable friends, and not one, but four sisters who cared about him. He'd fought long and hard, and vowed that he'd protect this peace with all he had. Add in the likely possibility that he and Asuka might be reunited with their mothers at some point-which was becoming more and more of a possibility each day-and Shinji felt extremely lucky to be where he was at the moment. Rei, in her own way, felt the same, looking back on where she'd come from and where she was at now.

Most importantly, both siblings were looking forward to where their lives would go, regardless of what happens.

**END Part 3.**


End file.
